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Guinea started without influential midfielder Naby Keita after his recent injury troubles but went ahead through Sory Kaba's confident finish on 34 minutes.
Indian Ocean islanders Madagascar, who were the first qualifiers for this year's tournament, replied early in the second half through Anicet Andrianantenaina.
They promptly took the lead when Charles Andriamahitsinoro produced a nerveless finish after latching onto a hopeful punt forward 10 minutes after half-time, but Francois Kamano salvaged a point for Guinea from the penalty spot following a foul on captain Ibrahima Traore.
Guinea failed to qualify for the 2017 edition but have made the quarter-finals in four of their past five appearances, although Keita was only fit enough for a place on the bench having yet to fully recover from a thigh injury that ruled him out of the Champions League final with Liverpool.
